1XPM

Crystal Structure of Staphylococcus aureus HMG-COA Synthase with HMG-CoA and Acetoacetyl-COA and Acetylated Cysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

3-hydroxy-3-methylglutaryl-CoA synthase intermediate complex observed in "real-time"

Theisen, M.J.Misra, I.Saadat, D.Campobasso, N.Miziorko, H.M.Harrison, D.H.T.

(2004) Proc.Natl.Acad.Sci.USA 47: 16442-16447

  • DOI: 10.1073/pnas.0405809101
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The formation of carbon-carbon bonds via an acyl-enzyme intermediate plays a central role in fatty acid, polyketide, and isoprenoid biosynthesis. Uniquely among condensing enzymes, 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase (HMGS) catalyzes the fo ...

    The formation of carbon-carbon bonds via an acyl-enzyme intermediate plays a central role in fatty acid, polyketide, and isoprenoid biosynthesis. Uniquely among condensing enzymes, 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase (HMGS) catalyzes the formation of a carbon-carbon bond by activating the methyl group of an acetylated cysteine. This reaction is essential in Gram-positive bacteria, and represents the first committed step in human cholesterol biosynthesis. Reaction kinetics, isotope exchange, and mass spectroscopy suggest surprisingly that HMGS is able to catalyze the "backwards" reaction in solution, where HMG-CoA is cleaved to form acetoacetyl-CoA (AcAc-CoA) and acetate. Here, we trap a complex of acetylated HMGS from Staphylococcus aureus and bound acetoacetyl-CoA by cryo-cooling enzyme crystals at three different times during the course of its back-reaction with its physiological product (HMG-CoA). This nonphysiological "backwards" reaction is used to understand the details of the physiological reaction with regards to individual residues involved in catalysis and substrate/product binding. The structures suggest that an active-site glutamic acid (Glu-79) acts as a general base both in the condensation between acetoacetyl-CoA and the acetylated enzyme, and the hydrolytic release of HMG-CoA from the enzyme. The ability to trap this enzyme-intermediate complex may suggest a role for protein dynamics and the interplay between protomers during the normal course of catalysis.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-hydroxy-3-methylglutaryl CoA synthase
A, B, C, D
396Staphylococcus aureus (strain MW2)Mutation(s): 0 
Gene Names: mvaS
Find proteins for A0A0H3K1U2 (Staphylococcus aureus (strain MW2))
Go to UniProtKB:  A0A0H3K1U2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAA
Query on CAA

Download SDF File 
Download CCD File 
A, B, C, D
ACETOACETYL-COENZYME A
C25 H40 N7 O18 P3 S
OJFDKHTZOUZBOS-CITAKDKDSA-N
 Ligand Interaction
HMG
Query on HMG

Download SDF File 
Download CCD File 
A, B, C, D
3-HYDROXY-3-METHYLGLUTARYL-COENZYME A
(S)-HMG-COA
C27 H39 N7 O20 P3 S
CABVTRNMFUVUDM-VRHQGPGLSA-I
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SCY
Query on SCY
A, B, C, D
L-PEPTIDE LINKINGC5 H9 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.119α = 90.00
b = 118.774β = 90.08
c = 121.304γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
DENZOdata reduction
BEASTphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description